Commit 9bc1f0c5 authored by Sean Solari's avatar Sean Solari
Browse files

Updated setup.py with extras_require

parent 12054b70
......@@ -8,7 +8,7 @@ then
exit 1
fi
rsync -vaRP docs src/expam test .gitignore .pyirc .readthedocs.yaml LICENSE MANIFEST.in pyproject.toml README.md setup.cfg setup.py buildandtwine.sh requirements.txt $EXPAM_PUBLIC_DIR
rsync -vaRP docs src/expam src/benchmark test .gitignore .pyirc .readthedocs.yaml LICENSE MANIFEST.in pyproject.toml README.md setup.cfg setup.py buildandtwine.sh requirements.txt $EXPAM_PUBLIC_DIR
echo "\nbuildandtwine.sh" >> $EXPAM_PUBLIC_DIR/.gitignore
echo "\n==================================\nLocal push completed successfully!\n==================================\n\nNow run build and run twine :)"
......@@ -109,16 +109,16 @@ setup(
#
python_requires=">=3.8",
install_requires=[
# "ete3",
# "PyQt5==5.12",
"numpy",
"matplotlib",
"pandas",
"psutil",
"requests",
# "sourmash",
"tables"
],
extras_require={
"treeplot": ["ete3", "PyQt5==5.12", "sourmash"]
},
#
# Cython modules.
#
......
......@@ -107,7 +107,8 @@ class CleanRaw(Process):
parts = line.strip().split('\t')
try:
parts[2] = self.taxid_map[parts[2]]
new_taxid = self.taxid_map[parts[2]]
parts[2] = new_taxid
except KeyError:
pass
......@@ -130,6 +131,8 @@ def make_results_compatible(db_path: str, results_config: ResultsPathConfig, bad
taxid_map = find_compatible_names(db_path, bad_taxids)
bad_taxids_set = set(bad_taxids)
print(taxid_map)
# Replace names in tax summary files.
summary_files = distribute(ls(results_config.tax, ext=".csv"), n)
procs = [CleanSummary(summary_files[i], bad_taxids_set) for i in range(n)]
......
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